Difference between revisions of "2013 AMS-536 Spring"
From Rizzo_Lab
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*[http://ringo.ams.sunysb.edu/index.php/Rizzo_Lab_Information_and_Tutorials Rizzo_Lab_Information_and_Tutorials] | *[http://ringo.ams.sunysb.edu/index.php/Rizzo_Lab_Information_and_Tutorials Rizzo_Lab_Information_and_Tutorials] | ||
<br> | <br> | ||
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| + | Cheat Sheet: [[Unix]], [[Vi]], [[C_Shell_Scripting]] | ||
== Schedule == | == Schedule == | ||
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| 2013.02.11 || Group Study || Visualization/analysis software, <br> VMD, MOE, Chimera, <br> Seawulf account setups, environments, shell scripting, misc unix | | 2013.02.11 || Group Study || Visualization/analysis software, <br> VMD, MOE, Chimera, <br> Seawulf account setups, environments, shell scripting, misc unix | ||
|- | |- | ||
| − | | 2013.02.13 || Group Study || | + | | 2013.02.13 || Group Study || Visualization/analysis software, <br> VMD, MOE, Chimera, <br> Seawulf account setups, environments, shell scripting, misc unix |
|- | |- | ||
| 2013.02.18 || Group Study || Tutorials: DOCK <br> individual project discussion [http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2012.02.13.ams536.joe.docking_intro.pdf Allen, W.] | | 2013.02.18 || Group Study || Tutorials: DOCK <br> individual project discussion [http://rizzo.ams.sunysb.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/Presentations/2012.02.13.ams536.joe.docking_intro.pdf Allen, W.] | ||
Revision as of 16:03, 15 January 2013
| Instructor | Dr. William J. Allen [631-632-8519, william.allen@stonybrook.edu]
Dr. Robert C. Rizzo [631-632-8519, rizzorc@gmail.com] |
|---|---|
| Course No. | AMS-536 / CHE-536 |
| Location/Time | Math Tower, Room S235 (COMPUTER LAB next to SINC site), Mon/Wed 2:20PM - 3:40PM |
| Office Hours | Anytime or by appointment, Math Tower, Room 3-129, Dept. of Applied Math & Statistics |
| Teaching Assistant | Lingling Jiang, Math Tower, Room 3-129, Dept. of Applied Math & Statistics |
Project Information
Project Approval Sheet
Oral Presentation Guidlines: These meetings should be formal and your chance to tell a complete story. Talks should be presented in PPT format and be 30 minutes long. The purpose of your talks is for you to clearly and concisely present your overall progress to date including appropriate background material and interpretation of your results. Talks should be arranged in the following order:
- Introduction/Background (include biological relevance)
- Specifics of Your System
- Computational Details (theory)
- Computational Details (system setup)
- Results and Discussion (include a critical interpretation of your results)
- Conclusions
- Future
- Acknowledgments
Final Report Guidelines and Example Final Papers
Tutorials, Software Links, and Other Relevant Class Information
Cheat Sheet: Unix, Vi, C_Shell_Scripting
Schedule
- Each participant please update the Wiki as required with the title of your talk.
- Please note that a doctors excuse will be required if you miss your scheduled oral presentation date because of illness.
| Date | Participant | Talk |
| 2013.01.28 | First Day of Class and Organizational Meeting Group Study |
Mathlab account setups, Unix and vi tutorials (1) http://www.ee.surrey.ac.uk/Teaching/Unix (2) At Linux command prompt type "vimtutor" (without the quotes) to start a built in tutorial for the text editor program called vi |
| 2013.01.30 | Group Study | Continue Mathlab account setups, Unix and vi tutorials (1) http://www.ee.surrey.ac.uk/Teaching/Unix (2) At Linux command prompt type "vimtutor" (without the quotes) to start a built in tutorial for the text editor program called vi |
| 2013.02.04 | Group Study | Visualization/analysis software, VMD, MOE, Chimera, Seawulf account setups, environments, shell scripting, misc unix |
| 2013.02.06 | Group Study | Visualization/analysis software, VMD, MOE, Chimera, Seawulf account setups, environments, shell scripting, misc unix |
| 2013.02.11 | Group Study | Visualization/analysis software, VMD, MOE, Chimera, Seawulf account setups, environments, shell scripting, misc unix |
| 2013.02.13 | Group Study | Visualization/analysis software, VMD, MOE, Chimera, Seawulf account setups, environments, shell scripting, misc unix |
| 2013.02.18 | Group Study | Tutorials: DOCK individual project discussion Allen, W. |
| 2013.02.20 | Group Study | Tutorials: DOCK individual project discussion |
| 2013.02.25 | Group Study | Tutorials: DOCK individual project discussion |
| 2013.02.27 | Group Study | Tutorials: DOCK individual project discussion |
| 2013.03.04 | Group Study | Tutorials: DOCK wiki editing |
| 2013.03.06 | Group Study | Tutorials: AMBER individual project discussion Jiang L. |
| 2013.03.11 | Group Study | Tutorials: AMBER individual project discussion |
| 2013.03.13 | Group Study | Tutorials: AMBER individual project discussion |
| 2013.03.18 | Spring Recess | Spring Recess |
| 2013.03.20 | Spring Recess | Spring Recess |
| 2013.03.25 | Group Study | Tutorials: AMBER individual project discussion |
| 2013.03.27 | Group Study | Tutorials: AMBER wiki editing |
| 2013.04.01 | Group Study | Project Setups / Troubleshooting |
| 2013.04.03 | Group Study | Project Setups / Troubleshooting |
| 2013.04.08 | TBD | Project Proposal |
| 2013.04.10 | TBD | Project Proposal |
| 2013.04.15 | TBD | Project Proposal |
| 2013.04.17 | Preliminary Report Due TBD |
Project Proposal |
| 2013.04.22 | TBD | Project Proposal |
| 2013.04.24 | TBD | Progress Report |
| 2013.04.29 | TBD | Progress Report |
| 2013.05.01 | TBD | Progress Report |
| 2013.05.06 | TBD | Progress Report |
| 2013.05.08 | Last Day of Class TBD |
Progress Report |
| 2013.05.15 | Final written report due by 5PM today. Late papers will not be accepted. See above for sample reports and detailed guidelines. | Give hard copy to Lingling Jiang (Math Tower room 3-129) and email electronic copy to rizzorc@gmail.com |
